Abstract
BackgroundPhages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS , Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.ResultsPHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype.ConclusionPHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.
Highlights
Phages, viruses that infect prokaryotes, are the most abundant microbes in the world
We present PHACCS (PHAge Communities from Contig Spectrum), an online computational tool to assess the diversity and structure of environmental viral communities from the contig spectrum of shotgun sequence data
For the MBSED community, the power law, lognormal, logarithmic and exponential distributions all tied for the best fit, whereas broken stick gave the worst fit
Summary
Viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). The study of environmental phage diversity, dynamics, and ecology requires growing prokaryotes on microbiology plates and infecting them with phages. This standard technique is limited by the fact that only a small fraction of environmental microbes are readily cultured [5] and that each phage species generally only has a very narrow number of possible microbial hosts [6]. Cultivating and observing phages do not permit to assess environmental phage diversity
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